rs2641670

Positions:

• chr16-84907374-G-A
• chr16-84907374-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_031476.4(CRISPLD2):​c.*732G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,412 control chromosomes in the GnomAD database, including 5,302 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.26 (5297 hom., cov: 33)
  • Exomes 𝑓: 0.18 (5 hom.)
• Consequence: CRISPLD2 NM_031476.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.477

Genes affected

CRISPLD2 (HGNC:25248): (cysteine rich secretory protein LCCL domain containing 2) Predicted to enable glycosaminoglycan binding activity. Involved in face morphogenesis. Located in transport vesicle. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CRISPLD2	NM_031476.4	c.*732G>A		3_prime_UTR_variant	15/15	ENST00000262424.10
CRISPLD2	XM_005256190.2	c.*732G>A		3_prime_UTR_variant	16/16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CRISPLD2	ENST00000262424.10	c.*732G>A		3_prime_UTR_variant	15/15	1	NM_031476.4	P4
CRISPLD2	ENST00000566165.1	c.121-12266G>A		intron_variant, NMD_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39355 AN: 152032 Hom.: 5281 Cov.: 33

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.292

GnomAD4 exome AF: 0.179 AC: 47 AN: 262 Hom.: 5 Cov.: 0 AF XY: 0.189 AC XY: 39 AN XY: 206

Gnomad4 AFR exome AF: 0.250

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.375

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.180

Gnomad4 OTH exome AF: 0.0714

GnomAD4 genome AF: 0.259 AC: 39409 AN: 152150 Hom.: 5297 Cov.: 33 AF XY: 0.261 AC XY: 19378 AN XY: 74372

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.240

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.289

Alfa AF: 0.218 Hom.: 2131

Bravo AF: 0.269

Asia WGS AF: 0.256 AC: 890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.8
DANN	Benign	0.54

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2641670; hg19: chr16-84940980;